Texture painting on the alpha channel (2.73)
The paint modes named Add Alpha and Erase Alpha may be what you are looking for.



If you are using a pen tablet then you can use the pen eraser to use Erase Alpha without having to change the blend mode in the UI.  There does not yet seem to be an alt key press that allows the pen eraser to toggle between Erase and Add.

Personally, I think the better way, for now, is to paint the texture the usual way and then use GIMP to add this texture to the Alpha channel of some other texture.  Blender does not really seem streamlined yet for working with and packing multiple images together in a convenient way. Maybe I'm just missing something and it's all there nicely workable already, blender can do lots of things that are not well documented :)

If you follow this link, I show how to add an image to the alpha channel of another image using GIMP.  Dotted line on curve?